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revision 1.1380 by jmc, Tue Feb 22 18:44:22 2011 UTC revision 1.1413 by jmc, Tue Apr 26 14:59:16 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint62w (2011/04/26)
8    o pkg/mom_fluxform:
9      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
10      - use parameter "sideDragFactor" in no-slip BC side-drag part.
11      - update output of exp. global_ocean.90x40x15
12    o pkg/mom_vecinv:
13      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
14    o update seaice exp.:
15      use more consistent parameter values (remove "backward compatability only":
16       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
17      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
18       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
19    o update test-exp global_ocean.90x40x15:
20      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
21      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
22      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
23      o turn on zStar & viscA4 in standard set-up (dir input/)
24        and update output files: output.txt & output.dwnslp.txt
25    o new AD-test experiment: obcs_ctrl
26      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
27    o pkg/dic:
28      fix two bugs in handling water vapour pressure in carbonate chemistry
29      and air-sea fluxes. Found by Val Bennington and Galen McKinley
30      (add DIC Option = WATERVAP_BUG to recover old results)
31      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
32    o adding allowInteriorFreezing option to check for water below freezing point
33      at depth and bring the negative heat anomaly to the surface level
34    o pkgs _fields_load:
35      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
36      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
37        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
38        rbcs to get interpolation weights and time reccord number.
39      - fix multi-threading in aim_fields_load.F
40      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
41    o external_fields_load:
42      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
43       interpolation weights) to use in a periodic time-series ; do not divide by
44       time-step to convert to integer:
45       - this fixes case where externForcingPeriod is not multiple of time-step
46          (Thanks to Christopher L. Wolfe)
47       - this fixes case where externForcingPeriod is an odd multiple of time-step
48         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
49      store index of time-record which is currently loaded:
50       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
51       - needed for the adjoint but not yet used because of extensive recomputations;
52         (to be fixed soon)
53    
54    checkpoint62v (2011/04/02)
55    o verification/1D_ocean_ice_column added to test Ian Fenty's
56      pkg/seaice_growth.F modifications for improving sea ice code differentiability
57    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
58      (new velocity statistics after changing maskInW & maskInS definition)
59    o pkg/generic_advdiff with OBCS:
60      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
61      equivalent to assumption of no tracer gradient outside the OB region.
62      This will affect the results if using obcs+biharmonic diffusion.
63      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
64    o pkg/obcs:
65      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
66      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
67      in Interior region. No impact on solution but affects Velocity monitor stats.
68    o pkg/ptracers (adjoint)
69      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
70      tape file for each tracer
71    o model/inc/src and pkg/autodiff: add parameters that allow to turn
72      of parts of the adjoint code at run time. For now, there are only
73      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
74      parameters are set in data.pkg.
75      This is the lazy coward's version of doing this, but still useful for
76      debugging. In order to do it right, everything needs to be moved to
77      pkg/autodiff.
78    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
79      the end; this fixes the adjoint balancing code for open boundaries.
80    o pkg/ctrl:
81      - change behavior of xx_${varname}period to be analogous to exf-conventions:
82        xx_${varname}period =   0.,  means time-independent control part
83        xx_${varname}period = -12., means one-year-periodic monthly control part
84      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
85        clean up ctrl_init a little, remove unused variables
86      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
87      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
88    
89    checkpoint62u (2011/03/15)
90    o model/src:
91      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
92        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
93      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
94        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
95    o pkg/ctrl/obcs/ecco:
96      - remove obsolete, unused, and partially broken code:
97        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
98        ALLOW_CTRL_OBCS_BALANCE
99      - put a stop statement into ecco/cost_obcsvol.F, but also add
100        cost_obcsvol to ecco_ad_diff.list
101    o pkg/ecco: fix counting cost function contributions for obcs (code
102      by Matt M.) and diffkr for diagnostics
103    o pkg/ecco, pkg/ctrl, pkg/grdchk:
104      add cost penalty terms for initial uvel, vvel, eta controls
105      and I/O for prior error files
106    o pkg/mdsio:
107       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
108       (new argument) to check for tiled file in mdsioLocalDir : this fix the
109       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
110    o pkg/ctrl:
111     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
112       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
113       unused and superfluous variables
114     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
115    o pkg/ecco
116     - enable adjoint of Stevens OB
117    o pkg/ctrl/ecco/grdchk:
118      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
119        Fortunately, we do not have any tests for the numerous cpp-flagged
120        option of "obcs as control parameters" so we will never know
121        if this is an improvement (but at least now things compile).
122      - remove an obsolete initialization from ecco_cost_init_barfiles.F
123      - fix some problems within never used ifdefs to make the code compile
124    o pkg/obcs:
125     - Refine Interior mask definition to work with more complex OB (e.g.
126       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
127       read in Interior mask from file. Check if Interior mask is consistent
128       with OB list of indices.
129    o pkg/seaice
130     - beginning code for a seaice tracer package,
131       but currently only used for seaice age: SEAICE_AGE
132       SEAICE_num = 4
133       iTracer = 1: area-weighted ice age
134               = 2: volume-weighted ice age
135               = 3, 4: template for one-year vs. multi-year ice
136       data.seaice has new namelist SEAICE_PARM03 for arrays related to
137       SEAICE_num
138    
139    checkpoint62t (2011/03/05)
140    o pkg/obcs:
141     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
142       then normal component. This ensures that the normal component is set
143       correctly even when it conficts with tangential setting from an other OB.
144       Affects results of test-experiment seaice_obcs: update the output.txt
145    o pkg/obcs:
146     - add code to monitor statistics of dynamical fields at OB.
147     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
148       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
149       - change default: balance the Net inflow through all OB (instead of balancing
150         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
151     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
152       to match Nortern OB inflow (OBCS_balanceFacN=0).
153    o pkg/seaice:
154     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
155    o pkg/seaice (seaice_growth v 1.113):
156     - reverting seaice_growth to v 1.111 in order to have code with exact bit
157       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
158       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
159       runtime flag SEAICEareaFormula is kept but is inactive
160  o model/src:  o model/src:
161   - add new param to scale curvilinear grid distance and area when using   - add new param to scale curvilinear grid distance and area when using
162     a different sphere radius from the grid-files.     a different sphere radius from the grid-files.
163   - test/check multi-threads EXCH applied to local variable (cg2d_x)   - test/check multi-threads EXCH applied to local variable (cg2d_x)
164    o adjoint:
165     - enable adjoint of Stevens OB
166     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
167       (a bit delicate because of potentially modified adj. common block structure;
168       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
169    
170  checkpoint62s (2011/02/15)  checkpoint62s (2011/02/15)
171  o pkg/seaice:  o pkg/seaice (seaice_growth v 1.112):
172   - introduce SEAICEareaFormula run time parameter, which selects the recipe for   - introduce SEAICEareaFormula run time parameter, which selects the recipe for
173     computing the ice cover tendency from effective thickness tendencies. Include     computing the ice cover tendency from effective thickness tendencies. Include
174     Ian Fenty's formula.     Ian Fenty's formula.
# Line 21  o pkg/gmredi: Line 179  o pkg/gmredi:
179   - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code   - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
180     from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;     from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
181     add a verification test-run (front_relax.bvp) to test GM_useBVP.     add a verification test-run (front_relax.bvp) to test GM_useBVP.
182  o pkg/seaice:  o pkg/seaice (seaice_growth v 1.111):
183   - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.   - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
184   - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to   - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
185     also melt ice.     also melt ice.
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